Revisiting the number of self‐incompatibility alleles in finite populations: From old models to new results

Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimat..., Codes and datasets for generating the figures in the main text and the Supplementary Information of the manuscript entitled \"Revisiting the number of self-incompatibility alleles: from old models to new results\" published in the Journal of Evolutionary Biology (https://doi.org/10.1111/jeb.14061). Version Update June 2024: There was a small mistake in the code that has been corrected now. The published figures had to be corrected, which can be found here: doi:10.1093/jeb/voae059/7685015., Generally, the code is structured per figure in the manuscript, i.e., all code to reproduce Figure X in the manuscript is contained in the folder labeled \"FigureX\". However, data and processing files need to be downloaded separately. Then the data needs to be copied into the respective folders of the software to run the codes. I am sorry for this complication, I do not like it either., # Revisiting the number of self‐incompatibility alleles in finite populations: From old models to new results [https://doi.org/10.5061/dryad.0zpc86712](https://doi.org/10.5061/dryad.0zpc86712) Data files are simulations from C++ code, which are used to produce the figures in the manuscript [https://doi.org/10.1111/jeb.14061](https://doi.org/10.1111/jeb.14061)\ To reproduce the figures, a Python code is used. Unfortunately, the code to create the data files and to reproduce the figures had to be isolated from the data files (dryad asked me to do this...). The \"software\" files are found here: [https://zenodo.org/records/6983482]() ## Description of the data and file structure File List: Folder structure to reproduce the figures in the main text and supplementary material of the corresponding publication, published in the Journal of Evolutionary Biology (2022). Fig1 folder: stationary distribution of self-incompatibility alleles, theory vs. numerical simulation Fig2 folder: number of...在配子体自交不亲和（gametophytic self-incompatibility, GSI）系统中，植物在自交不亲和位点（self-incompatibility locus, S-locus）呈杂合状态，仅能被携带该位点不同等位基因的花粉授粉。一个多世纪以来，学界围绕配子体自交不亲和种群中等位基因多样性的正确建模方式展开了激烈争论，且该问题始终未得到正式解决。 本研究从个体基模型出发，推导了Fisher（1958）提出的确定性动力学模型，并计算了稳态S等位基因频率分布。研究发现，Wright（1964）提出的稳态分布与我们的理论预测高度吻合，这与此前的数值验证结果一致。此外，我们近似计算了新S等位基因的入侵概率，该概率与现存S等位基因数量呈反比关系。最后，我们利用稳态等位基因频率分布，基于实验获得的等位基因频率谱估算植物种群规模，以此补充了现有估算方法…… 本研究配套的代码与数据集可复现发表于《进化生物学杂志（Journal of Evolutionary Biology）》的论文《重新审视自交不亲和等位基因的数量：从旧模型到新成果》（https://doi.org/10.1111/jeb.14061）正文中的所有图表及补充材料内容。 版本更新 2024年6月更新：此前代码中存在一处微小错误，现已修正。已发表的图表也需同步更正，更正后的图表可通过以下链接获取：doi:10.1093/jeb/voae059/7685015。 总体而言，代码按照论文中的图表进行模块化组织，即复现论文中第X幅图表的所有代码均存放于标注为"FigureX"的文件夹中。不过，数据文件与处理脚本需单独下载，且需将数据复制至对应软件的指定文件夹后方可运行代码。对于由此带来的操作复杂度，我们深表歉意，此并非我们所愿。 # 重新审视有限种群中的自交不亲和等位基因数量：从旧模型到新成果 [https://doi.org/10.5061/dryad.0zpc86712] 数据文件由C++代码生成的模拟结果构成，用于复现上述发表于《进化生物学杂志（Journal of Evolutionary Biology）》（2022年）的论文中的图表（https://doi.org/10.1111/jeb.14061）。复现图表需使用Python代码。遗憾的是，由于Dryad数据仓储（Dryad）的要求，生成数据文件与复现图表的代码需与数据文件分离。"软件"文件可通过以下链接获取：[https://zenodo.org/records/6983482]() ## 数据与文件结构说明 本数据集的文件目录结构可用于复现对应发表论文（2022年发表于《进化生物学杂志（Journal of Evolutionary Biology）》）的正文及补充材料中的所有图表。 - Fig1文件夹：自交不亲和等位基因的稳态分布：理论预测与数值模拟对比 - Fig2文件夹：用于生成……